R package wrapping the GS3 program for genomic selection (http://genoweb.toulouse.inra.fr/~alegarra/).
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README.md

Package "rgs3"

This directory contains the rgs3 package for the R software environment. This package wraps the GS3 program for genomic prediction and selection. See the web page from Andrés Legarra for more information.

The rgs3 package is available under a free software license, the GNU Public License (version 3 or later). See the COPYING file for details. The copyright is owned by the INRA.

The content of this directory is versioned using git, the central repository being hosted here, on GitHub, and the institutional repository being hosted there, on SourceSup.

Installation

Before installing the rgs3 package, the latest version of the GS3 program should already be installed on your computer (see on GitHub). More precisely, the executable should be present in your PATH, under the name gs3 for Unix-like operating systems (GNU/Linux, Mac OS) and gs3.exe for Microsoft Windows.

  • On Unix-like operating systems, you can save the executable in a new directory named bin in your home directory, and then add the path to this new directory to the environment variable PATH (use your ~/.bash_profile).

  • On Windows, you can save the executable in a new directory named GS3, for instance in C:\Program Files, and then add the path to this new directory to the environment variable Path (go to Configuration parameters -> System -> Advanced, or something similar).

To check if R properly detects the new directory, open a new R session, and call Sys.getenv("PATH"). To check if the executable is found in your PATH, open a new R session, and call system("gs3") (or system("gs3.exe") for Windows).

Then, to install the rgs3 package, the easiest is to download the released .tar.gz from SourceSup here, open a R session and run the following command:

install.packages("/path/to/rgs3_<version>.tar.gz", repos=NULL, type="source")

You can also install the latest version of the source code directly from GitHub, by opening a R session and running the following commands:

library(devtools) # can be installed from the CRAN
install_github("INRA/rgs3", build_vignettes=TRUE)

Note that creating the vignettes may take a couple of minutes.

Once this is done, the rgs3 package should be available on your computer.

Usage

Once the rgs3 package is installed on your computer, it can be loaded into a R session:

library(rgs3)
help(package="rgs3")
browseVignettes("rgs3")

Citation

As a lot of time and effort were spent in creating the GS3 program, please cite it when using it for data analysis:

Legarra, A., Ricard, A., Filangi, O. GS3, a  software  for  genome-wide genetic evaluations and validations. 2014.

You should also cite the rgs3 package:

citation("rgs3")

See also citation() for citing R itself.

Issues

When encountering a problem with the package, you can report issues on GitHub directly (here). Remember to copy-paste the output of sessionInfo() to help efficiently diagnose the problem and find a solution.

Contributing

You can contribute in various ways:

  • report an issue (online, see the above section);

  • suggest improvements (in the same way as issues);

  • propose a pull request (after creating a new branch).